diff --git a/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py b/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py
index c44772c63a05dc54d31fca24dd42f2b64d8af968..bdf94353e953e4b7a5daaf5911b557501db43d64 100644
--- a/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py
+++ b/plasmid/source/core-plugins/petermigration/1/dss/drop-boxes/petermigration/migration.py
@@ -61,7 +61,7 @@ def setEntityProperties(tr, definition, entity, properties):
vocabulary.addTerm(term)
#Uses new vocabulary term
propertyValue = codeToUse
- print repr(entity.getCode() + ", CREATED FOR VOCABULARY: " + propertyDefinition[4] + ", FOUND VALUE: " + labelToUse + ", NEW TERM WITH CODE: " + codeToUse)
+ #print repr(entity.getCode() + ", CREATED FOR VOCABULARY: " + propertyDefinition[4] + ", FOUND VALUE: " + labelToUse + ", NEW TERM WITH CODE: " + codeToUse)
if propertyDefinition is not None: #Sometimes special fields are added for other purposes, these should not be set
entity.setPropertyValue(propertyCode, propertyValue)
@@ -203,30 +203,32 @@ class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
entityCodeFieldName = None
def init(self):
+ print "Reading boxes for: " + self.__class__.__name__
emptyBox = 0
boxes = {}
EntityAdaptor.init(self)
preparedStatement = self.connection.prepareStatement(self.selectBoxQuery)
result = preparedStatement.executeQuery()
while result.next():
- entityId = unicode(entityIdFieldName)
+ entityId = unicode(result.getString(self.entityIdFieldName))
if entityId is not None:
if entityId in sampleID2Sample:
- antibodyNumber = sampleID2Sample[entityId][entityCodeFieldName]
- values = {}
- values["STORAGE_NAME"] = result.getString("location")
- values["STORAGE_ROW"] = None
- values["STORAGE_COLUMN"] = None
- values["STORAGE_BOX_NAME"] = result.getString("box label")
- values["STORAGE_USER"] = result.getString("frozen by")
- values["STORAGE_BOX_POSITION"] = result.getString("position")
-
- allboxes = []
- if antibodyNumber in boxes:
- allboxes = boxes[antibodyNumber]
- else:
- boxes[antibodyNumber] = allboxes
- allboxes.append(values)
+ antibodyNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
+ if antibodyNumber is not None:
+ values = {}
+ values["STORAGE_NAME"] = result.getString("location")
+ values["STORAGE_ROW"] = None
+ values["STORAGE_COLUMN"] = None
+ values["STORAGE_BOX_NAME"] = result.getString("box label")
+ values["STORAGE_USER"] = result.getString("frozen by")
+ values["STORAGE_BOX_POSITION"] = result.getString("position")
+
+ allBoxes = []
+ if antibodyNumber in boxes:
+ allBoxes = boxes[antibodyNumber]
+ else:
+ boxes[antibodyNumber] = allBoxes
+ allBoxes.append(values)
else:
#The antibody is not there. What the *#%$&
emptyBox += 1
@@ -236,17 +238,14 @@ class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
print "Not found: " + str(emptyBox)
- for antibodyCode, allAntibodyBoxes in boxes.iteritems():
+ for entiyCode, allBoxes in boxes.iteritems():
self.addEntity({
- "ANTIBODY_ID_NR" : antibodyCode,
- "*BOXESLIST" : allAntibodyBoxes
+ "*CODE" : entiyCode,
+ "*BOXESLIST" : allBoxes
})
result.close()
preparedStatement.close()
-
- def addEntity(self, values):
- self.entities.append(AntibodyBoxOpenBISDTO(values, self.definition))
##
## Antibodies
@@ -269,53 +268,10 @@ class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
def getIdentifier(self, tr):
return self.values["ANTIBODY_ID_NR"]
-class AntibodyBoxAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- emptyAntibodyBox = 0
- antibodyBoxes = {}
-
- self.selectQuery = "SELECT * FROM \"antibody boxes\""
- EntityAdaptor.init(self)
-
- preparedStatement = self.connection.prepareStatement(self.selectQuery)
- result = preparedStatement.executeQuery()
- while result.next():
- antibodyID = unicode(result.getString("antibody ID"))
- if antibodyID is not None:
- if antibodyID in sampleID2Sample:
- antibodyNumber = sampleID2Sample[antibodyID]["ANTIBODY_ID_NR"]
- values = {}
- values["STORAGE_NAME"] = result.getString("location")
- values["STORAGE_ROW"] = None
- values["STORAGE_COLUMN"] = None
- values["STORAGE_BOX_NAME"] = result.getString("box label")
- values["STORAGE_USER"] = result.getString("frozen by")
- values["STORAGE_BOX_POSITION"] = result.getString("position")
-
- allboxes = []
- if antibodyNumber in antibodyBoxes:
- allboxes = antibodyBoxes[antibodyNumber]
- else:
- antibodyBoxes[antibodyNumber] = allboxes
- allboxes.append(values)
- else:
- #The antibody is not there. What the *#%$&
- emptyAntibodyBox += 1
- else:
- #The antibody is not there. What the *#%$&
- emptyAntibodyBox += 1
-
- print "Antibody not found: " + str(emptyAntibodyBox)
-
- for antibodyCode, allAntibodyBoxes in antibodyBoxes.iteritems():
- self.addEntity({
- "ANTIBODY_ID_NR" : antibodyCode,
- "*BOXESLIST" : allAntibodyBoxes
- })
-
- result.close()
- preparedStatement.close()
+class AntibodyBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"antibody boxes\""
+ entityIdFieldName = "antibody ID"
+ entityCodeFieldName = "ANTIBODY_ID_NR"
def addEntity(self, values):
self.entities.append(AntibodyBoxOpenBISDTO(values, self.definition))
@@ -323,7 +279,7 @@ class AntibodyBoxAdaptor(FileMakerEntityAdaptor):
class AntibodyBoxOpenBISDTO(OpenBISDTO):
def write(self, tr):
- sample = getSampleForUpdate("/INVENTORY/"+self.values["ANTIBODY_ID_NR"], None, tr)
+ sample = getSampleForUpdate("/INVENTORY/"+self.values["*CODE"], None, tr)
#Delete old boxes
for boxNum in range(1, definitions.numberOfStorageGroups+1):
for propertyCode in definitions.stogageGroupPropertyCodes:
@@ -353,7 +309,7 @@ class AntibodyBoxOpenBISDTO(OpenBISDTO):
sample.setPropertyValue(propertyCode + "_" + str(boxNum), propertyValue)
def isBoxPressent(self, boxSignature, tr):
- sample = getSampleForUpdate("/INVENTORY/"+self.values["ANTIBODY_ID_NR"], None, tr)
+ sample = getSampleForUpdate("/INVENTORY/"+self.values["*CODE"], None, tr)
if sample is not None:
for boxNum in range(1, definitions.numberOfStorageGroups+1):
storedSignature = "";
@@ -592,14 +548,14 @@ fmConnStringServer = "jdbc:filemaker://fm.ethz.ch/"
fmUserServer= "sistemp"
fmPassServer = "ibcimsb2014"
-#adaptors = [#AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
- #AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
+adaptors = [AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
+ AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
#CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"),
#PlasmidAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmids_Peter"),
#StrainAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strains_Peter"),
#SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
- #ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),]
-adaptors = [OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
+ #ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
+ #OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
def createDataHierarchy(tr):